That means that by the end of summer all fish used in sushi, sashimi, tartare and other popular raw dishes will make a pit stop in the freezer before they end up on diners’ plates.

Though some customers might blanch at the idea that their coveted crudo and sashimi — sometimes costing hundreds of dollars — emerged from a deep freeze, the truth is that many chefs in the city’s top restaurants have long used frozen fish to prevent serving their raw fare with a side of pathogens.

“We purposely deep-freeze at negative 83 degrees, and we use one of those medical cryogenic freezers,” said Yuta Suzuki, vice president of Sushi Zen, a popular Times Square restaurant. “This way, it’s kind of like cooking, but instead of using heat we use freezing to remove parasites or bacteria on the outer surface.”

Even the New York City chapter of the New York State Restaurant Association, which had complained about the regulations at a health department hearing in January, has reversed course. Now that the regulations have been stripped of certain record-keeping requirements that the association considered onerous, establishments serving raw fish should be able to handle the change, James W. Versocki, a legal counselor for the group, said.

“By all indications, everyone will be enjoying the same quality of sushi,” Mr. Versocki said, who noted that the vast majority of fish is already flash frozen at some point in the supply chain.

The websites and menus for some of the city’s most expensive restaurants are often masterpieces of obfuscation when it comes to the word “fresh.” Even at Masa, which touts ingredients “only in their freshest most delicious state” for its $450 meals, chef Masayoshi Takayama has been known to occasionally opt for frozen fish. Naomichi Yasuda, whose restaurant, Sushi Yasuda, consistently ranks among the city’s best, has been extolling the merits of freezing fish for years. Not only does frozen fish come free of parasites, it is also cheaper, available out of season, and, in some cases, tastier. Plus, most diners are none the wiser.

“I’m pretty sure our customers are not able to tell,” Mr. Suzuki said, who noted that Sushi Zen doesn’t keep any of its fish raw.

The Health Department regulation stipulates that fish will require a minimum freezer storage time of anywhere from 15 hours to one week, depending on the temperatures used in the freezing and storage process. Several types of seafood are exempt from the rule, including shellfish, farm-raised fish and certain types of tuna.

National health agencies do not regularly track the cases of illnesses caused by eating raw fish, said Dr. Susan Montgomery, an epidemiologist at the Centers for Disease Control and Prevention, adding, “These infections are rare in the United States and generally aren’t fatal.”

Still, the city’s health department believes it cannot be too careful. Though the regulations do not require restaurants to advertise that their raw fish dishes were made from previously frozen ingredients, another new rule aims to make sure that customers know that there can be a downside to their raw fish cravings. Beginning in 2016, restaurants will have to put in print that raw and undercooked foods can be hazardous to one’s health.

For most restaurants, Mr. Versocki said, “the only change might be a new menu.”